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PaDEL Issue

Member for

2 years 6 months holyone2

I'd like to read a SMILES or SDF file in and used PaDEL to generate descriptors however

a) When using PaDEL's own Compounds Reader to read an SDF file I get the error:
"ERROR Compounds Reader     2:15       Execute failed: Error while writing to buffer, failed to write to file "knime_container_20170720_6246293811033658750.bin.gz": org.openscience.cdk.knime.type.CDKCell cannot be cast to org.openscience.cdk.knime.type.CDKCell"

b) I can read in SMILES,

File Reader -> RDKit From Molecule -> RDKit Salt Stripper -> RDKit Add Hs - > RDKit Generate Coords -> RDKit Optimize Geometry -> (PaDEL's own) Molecule to CDK --> PaDEL descriptor I get:
"ERROR PaDEL-Descriptor     2:14       Execute failed: org.knime.core.data.MissingCell cannot be cast to org.openscience.cdk.knime.type.CDKCell"

Does anyone know how I can resolve this issue? 

Kind Regards,

Ben

Comments
Wed, 07/26/2017 - 10:43

Member for

4 years 9 months

jonfuller

Hi Ben,

I don't have the PaDEL nodes installed so I couldn't confirm, but I'd recommend directly contacting the PaDEL node developers. Perhaps there is a version incompatibility with the CDK libraries being used.

Best,

Jon

Mon, 08/07/2017 - 10:53

Member for

8 years 6 months

swebb

I don't think you will get an support from the PaDEL developers as to the best of my knowledge they still haven't fixed their incompatibility with the KNIME CDK contribution. 

You may get lucky by filting out your missing values in advance as that seems to be part of the problem.

Cheers

Sam

Tue, 01/23/2018 - 09:43

Member for

9 years 4 months

gdurst

I am having the same problems and getting errors as Ben above from 6 months ago...

No matter how I prepare ligand structures in KNIME, (and always ending with the PaDEL supplied "Molecule to CDK" node) the PaDEL node always gives the error: Execute failed: ("ArrayIndexOutOfBoundsException): -1"

I also have no success with the "Compounds Reader" node packaged with PaDEL, it gives:

"Execute failed: Error while writing to buffer, failed to write to file "knime_container_20180123_3375941497910809366.bin.gz": org.openscience.cdk.knime.type.CDKCell cannot be cast to org.openscience.cdk.knime.type.CDKCell")

It's a pity as the calculation of all these properties is very useful. So far my only solution is to use the Linux command line which reads any of the above generated molecule files just fine. I guess their KNIME node doesn't use the same code (?)

It would be so nice to be able to pipeline this calculation into my workflows. Does anyone have a better idea on how to fix this?

Greg